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Status
Public on Jul 09, 2008
Title
Pneumonia (Viro3P12-245)
Sample type
RNA
Source name
RdABC amplified RNA from Nasal Lavage
Organism
Viruses Characteristics
Pneumonia
Extracted molecule
total RNA
Extraction protocol
RNeasy followed by DNAse treatment
Label
Cy3
Label protocol
Rd C Cy3 incorporation
Hybridization protocol
standard overnight hybridization
Scan protocol
Axon 4000 scanner
Description
RdABC amplified RNA from Nasal Lavage
Data processing
Median feature intensity minus median background intensity. The data analysis software used is E-Predict, which normalizes the data using a variety of measures: sum, quadratic, unit-vector, or no normalization (please see Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL.E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.Genome Biol. 2005;6(9):R78. Epub 2005 Aug 30). E-Predict is public access. For the purposes of this paper, sum-normalized intensities were used in the analysis.
Submission date
Jan 28, 2008
Last update date
Jul 09, 2008
Contact name
Joe DeRisi
E-mail(s)
joe@derisilab.ucsf.edu Phone
415-476-4132
URL
http://derisilab.ucsf.edu Organization name
University of California, San Francisco
Department
Biochemistry and Biophysics
Lab
Joseph DeRisi Laboratory
Street address
City
San Francisco
State/province
CA
ZIP/Postal code
94107
Country
USA
Platform ID
GPL3429 Series (1)
Data table header descriptions ID_REF VALUE same as UNF_VALUE but with flagged values removed
CH1_MEDIAN Channel 1 intensity median
CH1_MEAN Channel 1 intensity mean
CH1_SD Channel 1 intensity standard deviation
CH1_BGD_MEDIAN Channel 1 background intensity median
CH1_BGD_MEAN Channel 1 background intensity mean
CH1_BGD_SD Channel 1 background intensity standard deviation
CH1_NET_MEDIAN Channel 1 net intensity median
CH1_NET_MEAN Channel 1 net intensity median
FLAG GenePix spot flag
UNF_VALUE Channel 1 net intensity median (same as CH1_NET_MEDIAN)
Data table ID_REF VALUE CH1_MEDIAN CH1_MEAN CH1_SD CH1_BGD_MEDIAN CH1_BGD_MEAN CH1_BGD_SD CH1_NET_MEDIAN CH1_NET_MEAN FLAG UNF_VALUE 1
31
70
70
18
39
40
9
31
31
31
2
43
85
87
21
42
45
20
43
45
43
3
41
84
83
11
43
44
12
41
40
41
4
39
86
84
17
47
47
10
39
37
39
5
47
86
87
20
39
41
9
47
48
47
6
43
89
88
18
46
48
11
43
42
43
7
37
77
77
19
40
40
9
37
37
37
8
38
83
84
20
45
47
11
38
39
38
9
35
75
77
18
40
41
8
35
37
35
10
48
91
90
18
43
45
10
48
47
48
11
462
513
501
142
51
52
15
462
450
462
12
1351
1401
1356
524
50
52
20
1351
1306
1351
13
33
79
79
12
46
57
78
33
33
33
14
56
97
97
21
41
42
10
56
56
56
15
123
170
167
47
47
58
87
123
120
123
16
30
78
86
48
48
57
86
30
38
30
17
37
89
85
20
52
53
12
37
33
37
18
34
86
86
22
52
64
99
34
34
34
19
56
136
132
21
80
84
19
56
52
56
20
63
164
168
35
101
102
18
63
67
63
21888 803 Kbytes .Supplementary file Size Download File type/resource GSM260195.gpr.gz
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